I am interested in running your Krypteia program and want to buy the 5/3/1 forever book. I have two questions:
1. Is there a way to run Kypteia alongside Muay Thai 2-3x a week? If not is there another program I can run that is compatible?
2. Is it outlined in the book?
Let's start with whether or not the Krypteia program is suitable for someone who is also doing Muay Thai 3x's a week. Where this is the program I recommend to most athletes, the only answer any outside person could honestly give this question is, "I don't know". This is because outside individuals have no idea of your training history, your in-season and off-season training as well as knowing your Muay Thai training AND your current training capacity. All of these things, and more, go into a total training program. That can't be stressed enough.
I did write a previous article called 5/3/1 and Coaching Athletes that I think you will find helpful. Also, an article from 2012 5/3/1 and Athletes. It has not been revised.
The other issue that should be addressed is why doesn't your Muay Thai instructor/school know what to do, or at least out-source the training? I find that total bush-league. Every sport understands the importance of G.P.P. and I don't know how you are supposed to compete in a sport without having some sort of guidance with your training (class-opening calisthenics is not adequate). Your instructor or coach should be more than qualified to handle this or point you in the direction of someone they trust and outsource to in this area.
Understand that training during the in-season requires a lot of "on the spot" changes and you must be able to adjust accordingly. This is why you work with someone personally to help guide you. Especially since your goal is to compete and win; not become a weight room champion.
Generally speaking, your weight training (anything other than your S.P.P. work) should be as little as possible while making the necessary gains. You shouldn't be doing marathon lifting sessions and they should be trimmed to only include the essentials. Remember that sport training is much different than powerlifting, bodybuilding, Olympic lifting and "just working out."
I highly advise you to find someone who knows your Muay Thai training and can help you devise a proper, periodized training program to compliment it. And again, if your current set-up refuses or denies this, it might be time to change. There is no excuse to not have access to this.